Heating Cy labeled oligos to 94⁰C will not cause degradation or loss of the Cy dye. Cy labeled oligos are frequently used in PCR based applications without problems. Cy dyes are very susceptible to damage by ozone, however. They are also known to have some self-quenching problems (see Gruber et al (2000) Bioconjugate Chem 11:696-704.
) For storage we recommend keeping Cy labeled oligos in a neutral pH solution at -20⁰C.